Plotopterids (Aves: Plotopteridae) are extinct flightless birds that were endemic to the North Pacific Ocean. As flightless, wing‐propelled diving birds they exhibit similar skeletal morphology to Sphenisciformes (penguins), especially in their wings. In contrast to the similarity, Plotopteridae have been placed in (traditional) Pelecaniformes in most palaeontological and phylogenetic studies, based on shared characters that are absent in penguins. The postcranial morphology of Plotopteridae has been well studied, but little is known about the cranial morphology, particularly the nervous system. The brain morphology of Plotopteridae, compared with other water birds, could prompt a reconsideration of those previous phylogenetic hypotheses, as the cranial morphology is conservative and could provide powerful signals for the phylogenetic reconstruction. In order to compare the brain morphology of Plotopteridae with that in other water birds (Ciconiiformes, Pelecaniformes, Suliformes, Procellariiformes, and Sphenisciformes), we generated virtual endocasts of Plotopteridae and extant water birds. We investigated the brain morphology of those birds using three‐dimensional geometric morphometric and linear measuring methods. The width of the cerebellum and the length of the floccular lobe varied considerably among water birds, and the relative lengths separate Procellariiformes + Sphenisciformes from Ciconiiformes + Pelecaniformes + Suliformes. The former group had a relatively wider cerebellum and longer floccular lobe, whereas the latter group had a relatively narrower cerebellum and shorter floccular lobe. The relative width of the cerebellum and length of the floccular lobe in Plotopteridae was comparable with that of the former group, in addition to many morphological similarities to the Sphenisciformes brain. On the basis of brain morphology alone, we dare not conclude that Plotopteridae forms a clade with, or belongs to, Sphenisciformes; however, the brain configuration of Plotopteridae is distinctly close to that of penguins, and could possibly reflect their phylogenetic relationship. © 2013 The Linnean Society of London